Naruto: Fallen Leaves
by SuperKayJin
Summary: Not all Leaves fall beside the Tree of their birth. The Whirlpool Country has risen and a dire warning of the end of the world is given. A New Era will be ushered in by the Greatest Shinobi of the Age... Uzumaki Naruto.
1. Ch 1: The Return

**NARUTO:**

**FALLEN LEAVES**

**CHAPTER ONE**

**NOT ALL LEAVES FALL**

A.N: I don't own Naruto.

Of all the Hidden Villages, Konoha was said to be the most beautiful. Nestled in the Heart of the Fire Country, it was surrounded by a great forest that gave rise to its name. Konoha, the Village Hidden Among the Leaves. Although the Fire Country was smaller than some of the other countries it had the greatest Hidden Village, Konoha and its greatness was due to the powerful Ninja it had produced; All the Hokage's were considered very powerful even among their counterparts. It had also birthed the Legendary Three Sannin, The White Fang, and other powerful Ninja.

Konoha had even survived an attack by the most powerful of the Biju, the Kyubi no Kitsune the fearsome Nine Tailed fox. It had been defeated by one man, who was arguably the greatest Ninja to ever live, and an infant. The Yondaime Hokage sealed the Demon Fox into a new born baby thus ending its rampage and setting the stage for a new generation of Konoha Shinobi to live. His last wish was for the child to be seen as a hero who protected the Village, and for him to be taken care of since he would effectively become an orphan.

His dying wish was not fulfilled and so the child grew up, feared and loathed by the very people he unknowingly protected. Despite this he overcame tremendous hardships and he finally became a Ninja, which to him was one step closer to fulfilling his dream of becoming Hokage.

He struggled and persevered, fighting powerful foes and never once losing sight of his dream. His first true failure came on the fateful day when he faced his symbolic brother, Uchiha Sasuke who tortured by his own demons had decided to leave Konoha. He managed to strike a line through his brother's Hitaite, and that one act proved to his brother and to himself that he was truly strong. That day was first taste of the pain that was betrayal.

That day he realized that Betrayal was the dark hearted slayer of faith.

Had the Yondaime not died he would have surely saved the boy from that pain but he was gone and the boy had to endure that pain. Greater than any loneliness, its venomous roots were planted that day and in the Village of Konoha those roots were unknowingly nurtured by a deep secret that was hidden from him.

Even in the encroaching darkness light still shone and it came in the form of a shy black haired, lavender-white eyed girl. Who helped him up when he fell, who accepted him for who he was, who supported him when he stumbled and who held him when he cried. So it was that light shone upon the boy, lifting his heart and strengthening his Spirit. Together they accomplished many things and so in time the boy truly saw the girl and the woman she would become and he confessed his love for.

So the boy gained true strength in that he had found his most precious person.

He was able to retrieve his brother and fulfil his promise of a lifetime.

It was soon after this that war broke out. The Sound Village led by Orochimaru launched an invasion to retrieve Uchiha Sasuke.

It was a hard fought battle, and no field had seen so many brave and powerful Konoha Shinobi assembled.

Greatest of all the Shinobi was the boy. The human sacrifice for the Nine Tailed Demon Fox.

Orochimaru's army, the forces of the Hidden Sound Village were thoroughly defeated and that boy stood above Orochimaru readying to deliver the killing blow but he hesitated as the Snake Sannin told him the truth about his heritage.

There can be no true rendition of betrayal, for the moment hides within itself, sudden, delivering such comprehension that one would surrender his or her soul to deny all that has come to pass. There can be no true rendition of betrayal, and thus the boy was grievously injured. The truth kept hidden for so long was finally revealed. The boy learned the names of his parents eighteen years after they had passed away. The last wound Orochimaru delivered was his most grievous. The Hidden Village of Konoha had lost its greatest hero.

The boy was named Uzumaki Naruto and on that day he and Hyuga Hinata disappeared.

--

**28 Years since the Yondaime died.**

_The Fifth Great Ninja War_

"Damn it" Konohamaru cursed under his breath as the large group of Cloud Ninja surrounded him and his small group.

They were on their way back home from a mission when they were ambushed by the Ninja on the border of the Fire Country. It was supposed to be a covert spying mission with few enemy confrontations but various skirmishes within the Lightening Country saw his Konoha Corps fighting a protracted battle and right now they were in need of rest and medical attention.

If Hanabi had not been hurt she would have been able to spot the ambush and they could have avoided the Ninja's. The Corps were a specialized unit he had created consisting of himself, Hanabi, Udon and Moegi. The original Konohamaru corps had always worked well together and with the addition of Hanabi their mission success rate had increased incredibly. They were all Jounin's and they would come together to fulfil specialized missions, that utilized all of their skills.

Even though he and Udon had taken down twenty Cloud Ninja they still outnumbered them greatly. Moegi had taken down a few who had thought she and Hanabi were easy targets, but it was still not enough.

Right now things looked a bit grim. He and Udon were low on Chakra and so the Cloud Ninja were not attacking with Taijutsu anymore. They were simply taking their distance and launching different Jutsu's at them forcing them to dodge and use chakra.

"You should have summoned Enma" Hanabi whispered from behind him. Her usual mocking tone was replaced by a wistful humorous one. Moegi had given her what Medical help she could and it seemed that she was finally on her feet, albeit barely. It was hardly enough to help in the battle and to tell the truth he did not even want her to enter the battle. He cared too much for her to see her fight in such a state.

No choice. He thought to himself.

He unbuttoned the collar of his Jounin jacket and reached inside. He then pulled at the chain he had hidden around his neck and on its end was a kunai.

He removed the chain and the kunai from around his neck and he then began to spin the weapon.

It was an unconventional kunai in the shape of a trident. It was also a bit heavier than the standard issue kunai but what was most striking about it was the design on the shaft.

There was a beautiful Kanji written in an ancient dialect that very few could interpret. It was a gift from his big brother and he clearly remembered the words spoken to him, long ago.

--

"You and me Konohamaru, we are brothers. We hold a deep bond and a strong rivalry. That is why I am giving this to you."

Konohamaru warily accepted the strange kunai from his big brother. It was very rare for him to be so serious and so the moment was leant even greater weight.

"I will always be there for you… never forget that"

"Hai big brother" and on impulse he embraced the Shinobi who had been such an important factor in his life.

--

It was the last time he had spoken to his brother because it was the day he disappeared. It was the final day of the war against Orochimaru.

The surrounding ninja seemed to be wary of the weapon but their numbers leant them a greater strength to stand and face the weary Konoha party. Not wanting to wait for him to do what he was doing the Ninja's attacked as one but Konohamaru pre-empted them and tossed the kunai between them and as one the Cloud Ninja's drew back.

"The kids got nothing" one of them said.

"Yeah let's finish them off and bring their heads back to the Village" even as he said this, they all attacked again.

--

Suddenly they all stopped in their tracks. An enormous pressure was pressing down upon all the Cloud Ninja on the field and most were struggling to breathe let alone stand. Curiously enough it did not affect the Konoha Nin who stood watching the scene.

A fierce wind then picked up blowing all of the Cloud Ninja away. The pressure did not ease up. There was confusion among their ranks but due to their high level of training they quickly regrouped and went into a defensive position.

"Kami" one of them said and they all followed his line of sight.

In the middle of the battlefield stood a tall figure wearing a deep red cloak, with Yellow flames stylized on the edges. The figures face was covered by a large hood and just above the hood the Onyx and platinum handle of a sword could be seen.

The figure did not radiate killer intent, nor did he emit large amounts of chakra, he simply stood between the two forces, Unmoving and unmovable.

Another figure had appeared in the midst of the Konoha Ninja. This one wore an Onyx cape that seemed to flow like liquid. Blue flames decorated the edges of the cloak and a matching hood hid the figures face. A long spear wrapped in a silver cloth was strapped to the figures back and she slowly removed it as she knelt over the female Konoha Nin who had been injured. The figures arms were extended and around the smooth delicate hands a green glow had appeared.

Those with sharp eyes were able to see the life return to the fallen girl and they realized to their shock that the woman was a Medic Nin.

It was clear in the way the man stood he was incredibly powerful and judging by the injured girl's recovery it was clear that the Medic Nin was extremely skilled.

"It's them!" One Cloud Ninja exclaimed, with an edge of hysteria in his voice. "Those two!" He began to back away and some of the others followed his lead.

"Cowards!" another shouted and he along with ten of his friends charged.

What followed happened so fast that none except the red cloaked figures partner could follow it. All ten had started moving only to see their life's blood spilling from their bodies. To the others it looked like the figure did not even move, yet ten of their comrades were dead. Clean cuts not delivered by a blade but by chakra. The only trace that the figure had moved was the swish of his cloak.

Some tried to run, but most of the Ninja accepted their fate, making peace with their gods and trying one last attempt at attack. One by one they died, their last sight was a pair of sapphire blue eyes.

--

"I should have never let her go" Neji cursed at himself. As the head of the Hyuga his duty was to ensure the continuation of the bloodline and even though the main house and branch houses had been removed it was still his responsibility, to follow in the footsteps of the Generations before.

Hanabi was young and head strong not easily bending to his wishes and those of her father, instead she sought her own path much like her sister… Hinata.

Two arms wrapped around his waist and the tension he was holding in evaporated.

"I won't say don't worry because I'm worried too, but she is a Ninja and she can take care of herself" Tenten said to him.

"Still, they've been gone a long time." He raised the point that was the source of his worry.

The Hyuga compound was quiet and so was most of the Village. It was an important day, and preparations were under way for a Grand festival. This day marked the 28th Anniversary of the day the Yondaime sealed the Kyubi and saved the Village. It also marked the 10th Anniversary of the day Orochimaru and the Sound Village were defeated.

The two started to head back inside the compound when the blue crystals they wore around their necks glowed.

Recognizing it as a summons from the Godaime Hokage the two disappeared in puffs of smoke.

--

Shikamaru's eyes snapped open and he looked towards the chair by the Shogi table in his bedroom. The blue crystal that hung from it was glowing and he knew what that meant.

"How troublesome" he grumbled.

He had been sleeping very nicely before he was awakened by the summons and he was a little put off by the idea of going to see the Hokage. This time he was not really lazy, he was well and truly tired. He had decided on having some fun by surprising his wife with a bouquet of flowers and a tender kiss on the cheek. That this would lead to them making love had not only crossed his mind but he was actually planning on it.

He carefully tried to get out of bed without disturbing his partner but unfortunately for him nothing got past her

"Going somewhere?" she asked

Shikamaru put on his clothes and approached the bed. He placed a kiss on her forehead and whispered.

"I've been summoned. Go back to sleep and I'll see you later"

She seemed to accept this with a smile and she drifted back to sleep. He brushed a stray lock of blonde hair. He liked it when it was down, instead of in those four pig tails but he would never tell her that.

This was one woman who was worth all the trouble.

He looked at the Shogi board and moved one piece, and then he took his necklace and made his way out of the window towards the Hokage monument.

--

Chouji was just sitting down to the large meal that Ino had made for him when he sensed the summons.

Ino also sensed the summons and she realized the dilemma they were in.

They either had to go and leave all this food behind or they could stay and incur the temper of the Hokage for being late.

Fortunately Chouji solved the dilemma. He pushed the plate of food away from him and he got up.

They both made their way out of their home and just before they left Ino saw Chouji give the food one last longing look.

--

Tsunade stood on top of the Hokage monument. She was surrounded by the elite Ninja of Konoha. Hatake Kakashi, Rin, Uchiha Sasuke, Haruno Sakura, Might Gai, Yuhi Kurenai, Nara Shikamaru, Yamanako Ino, Akimichi Chouji, Aburame Shino, Rock Lee, Inuzuka Kiba, Tenten and Hyuga Neji.

Jiraiya stood by her side as he had done since the battle with Orochimaru. They had finally accepted their pasts and they had built a future together. It was all for their son and their grandson.

"I will make this quick." She said to the gathered Shinobi. "I have been tracking the Konoha Corps since they started making their way back home. Hanabi was gravely injured and they were conducting a fighting withdrawal." She waited for her words to sink in. "As they approached the border they were ambushed by Cloud Ninja. Outnumbered they fought bravely and took down many of the enemies."

"Are they alright?" Ino asked the question on everybody's minds.

"I am not sure. There was a disturbance when Konohamaru used a kunai. He threw it into the ground and then my Jutsu was dispelled by an unknown force."

"Your mission is to go the border to find the fate of the Konoha Corps. Should you find an unknown enemy, engage it only to gauge its strength and motives. No heroic stands." The Toad Hermit finished with a wry smile.

"What is the classification of this mission and why does it require all of us." Shikamaru asked.

"This mission has been classified SS." Stunned silence followed her statement. "This is not based on any evidence but on a gut feeling. Those of you who do not wish to go can stay behind." She added knowing that none of them would.

She waited for a while and satisfied that none of them would pass on this mission she prepared to send them off.

"BOOOOOOOOOM!!"

The loud crash on the outskirts of the Village drew all of their attention. Dust and debris obscured whatever had caused the sound. All of the Ninja assumed a ready battle stance except herself and Jiraiya.

A wind picked up, blowing away the enormous dust…to reveal

The enormous Toad Boss Gamabunta.

"Neji, who is that?" The Hokage asked, her voice shaking.

"A powerful Shinobi wearing a red cloak" he stated and he was about to say more but he was interrupted.

"ROOOOOOOOAR!!" The sound echoed across the heavens above Konoha and more than one Villager quailed in their boots. The Large, green snake like Dragon broke through the clouds and landed next to the Toad.

For a moment all the Shinobi were too shocked to move.

"Neji, report" she snapped out the command.

"Yes Hokage-Sama. Another figure but this one is wearing a black cloak. I can also see Konohamaru, Hanabi, Udon and Moegi and they all seem alright."

"Can't you tell who the figures are?" Tenten asked her husband.

"No, I cannot see them clearly." All the Shinobi absorbed this information and the realization that these two were the power that Tsunade had sensed sunk in.

"No wonder it was an SS-Rank mission." Kakashi said in the silence.

"Who are they?" Chouji asked.

"Only one man alive is given the grace to ride atop the Toad Boss."

"Naruto…" the Hokage whispered her voice filled with hope and longing.

--

"I still don't know why I didn't get to ride with Naruto, on his toad." Konohamaru complained.

"Gaki!" The Toad Boss boomed. "Do you know who you're talking about? The Toad Boss Gamabunta is only ridden by one Shinobi! Remember that!"

Konohamaru jumped back shaking in fear.

"You shouldn't scare ones smaller than thyself Gamabunta-Sama.?" A soft but loud voice said.

"Serves him right thinking he can complain like that, I have had enough of smart mouthed brats to last me a life time, Ryushi." The Toad Boss grumbled.

"Konohamaru, you wait here to report to the Hokage about your mission." Naruto cut in. He bent down and whispered something to Gamabunta.

"Yare, Yare, if it wasn't for the things I've seen you do I would still think you're the same kid from all of those years ago. You're so childish sometimes, Naruto." Gamabunta said with an exhale of smoke punctuated by an exasperated sigh.

"But you're still going to do whatever it is he asked you Gamabunta-Sama." Hinata said with a smile.

"I guess it can't be helped. HERE WE GO NARUTO!!" A large force of chakra burst from Gamabunta and he leaped high into the air, briefly blotting out the sun and then he plummeted to the ground. The sudden eclipse caused some alarm among the citizens of Konoha and that alarm soon turned to concern as they saw the large toad falling upon…

Just as it was about to hit the first building, the Toad dispersed in an explosion of smoke that covered the whole Village.

"Thank you for your assistance, Ryushi" Hinata said.

"It is always a pleasure to assist you Hinata-Hime."

The large Dragon let the party climb down and it disappeared in a puff of smoke.

"I'll go find Naruto, see you later." Hinata said and then she went to Hanabi. "It was good to see you again Hanabi-Chan." Hinata hugged her little sister and then she disappeared into the Village.

"Why do we have to wait here to report to the Hokage? We could simply head to the Hokage Tower" Moegi suggested.

"That won't be necessary" Hanabi said.

"Why?"

"Because she is already here" Konohamaru answered.

In an instant the most powerful Shinobi in Konoha were assembled around them. Konohamaru immediately went down onto one knee, and his team-mates followed suit.

"Hokage-Sama, the mission was a success." He said in a formal tone.

"We can discuss that later. Who were the Shinobi who brought you here and where have they gone?" She asked.

Konohamaru was silent for awhile but he could not help the smile that came to his face. "Hokage-Sama, it was Uzumaki Naruto and Uzumaki Hinata. They have entered the Village but I cannot tell you their exact location."

"There's only one place he could be, judging by where Gamabunta dispersed." Jiraiya stated.

"ITADAKIMASU!!" someone in the Village screamed.

As one the Elite of Konoha disappeared in puffs of smoke and burst of leaves.

"In some ways, he is a bit predictable" Konohamaru said as he stood up and entered into the city.

Ichiraku Ramen was now a fully fledged restaurant serving other types of food but the small stand that had been a part of Konoha still existed as a place to get a good bowl of Ramen.

Tsunade and her group immediately went to the Ramen stand. Old Man Ichiraku still served customers with a smile but today his face was lit up with joy.

There were only two customers at the stand. One wore one wore an onyx cloak with blue flames on the hem and the other wore a deep red cloak with yellow flames licking its hem.

The backs of the cloaks held two different Kanji and they were ORDER and CHAOS respectively. For those in the Godaime's group who had studied the Ancient scripts, they were able to see the deeper meaning in the two symbols. Together they had formed the holiest symbol written in the old tongue.

BALANCE

The figures also had their hoods down and the one with an onyx cape had long flowing black hair and the one with the red cloak had spiky bright blonde hair. There were a pile of empty bowls next to the man with the red cloak and he seemed to be totally engrossed in his meal.

The woman was also eating but she was slower than him.

The two did not acknowledge the presence of the Shinobi who had gathered behind them. They just continued eating.

The Godaime and her group did not move, waiting for the pair to finish.

"Hey old man, that was some good ramen" the man said in a deep voice.

"Hai Ichiraku-Sama, I enjoyed it very much." The woman said in a soft voice.

The man reached into his cloak and they heard the clatter of coins.

The Godaime's eyes widened as she saw the gold coins being placed onto the counter.

"That's for my overdue tab" the man said.

The two then stood up as one. The woman was about to turn around when the man placed a hand on her arm. Intense chakra flooded the area and the two were gone.

"Family business" Jiraiya said and he placed a hand on Tsunade and they too disappeared.

AN: Chapter 1 Remixed.


	2. Ch2: Family Business

NARUTO:

**NARUTO:**

**FALLEN LEAVES**

**CHAPTER TWO**

**FAMILY BUSINESS**

AN: I do not own Naruto.

"I can't believe they're really here" Uchiha Sakura said in silence. "I almost thought we would never see them again".

Sasuke moved to his wife and placed a comforting hand on her shoulder.

"This is almost too good to be true, Naruto-kun and Hinata-chan are back-"

"That's where you're wrong" Konohamaru interrupted Tenten with a hint of sadness in his voice. "He's not here to stay. The way he put it, he's just passing through."

Everyone was silent after what Konohamaru said.

They all eventually found out why Naruto had left and so they understood even though they secretly hoped he would return.

"Some wounds never heal..." Kakashi said.

"So that was the son of the Yondaime." Rin said. "I never got a look at his face, but the hair is the same…"

"What I wouldn't give to be a fly on the wall, for the conversation between Naruto and his grandparents." Ino said.

"Intense won't even come close to describing that moment-" Shikamaru was interrupted by an enormous killing intent.

It was unlike anything they had felt before. The faces of the younger generation of Konoha Shinobi mirrored fear and shock but on the faces of the older generation there was another look… one of recognition.

"Kyubi" Kakashi said…

--

Naruto was standing upon the carving of the Yondaime. He then crouched down and placed a hand on the stone.

Naruto whispered something that Jiraiya couldn't hear.

Naruto then slowly stood up and as one he and Hinata turned to face them.

Jiraiya expected anger to show on his face but the bright blue eyes sparkled with laughter.

"Ohayo, Bachaan, Jiisan" Naruto said.

"Ohayo" Hinata said with a respectful bow.

He didn't know what he was expecting but this was definitely not it. He had expected shouting and swearing from Naruto, not a respectful greeting.

He also sensed the dismay in Tsunade but she quickly recovered.

"Ohayo, Naruto-kun, Ohayo Hinata-chan" Tsunade greeted in return.

"Ohayo" Jiraiya greeted.

Then Naruto brought his hands together in front of his abdomen. His hands glowed crimson and he then touched them to his abdomen.

A blind red light burst forth from Naruto.

The enormous killing intent that washed over him and Tsunade nearly brought them to their knees. Such a blatant display of the power he held in check was a clear message to Jiraiya and the people of Konoha.

When the power finally died down Jiraiya was able to see Naruto again. Hinata stood calmly at his side and he seemed perfectly normal.

"What was that for Naruto?" Tsunade asked.

"He felt like letting off a little steam." He calmly replied.

"Are you used to indulging him in such a way?" She asked.

"You'd be surprised at what I indulge him…." Naruto said quietly.

"How are our great grandchildren?" Tsunade asked.

"They are well, thank you" Hinata replied. A gentle breeze blew and the cloaks they were wearing fluttered slightly. Jiraiya glimpsed the swell of Hinata's stomach.

"I am still surprised that you have not stepped down yet. A Rokudaime Hokage is needed to help Konoha weather the Storm that is coming" Naruto said.

"I am holding that position until you decide to return for good Naruto." Tsunade replied.

"Unfortunately that will not be possible Tsunade-sama." Hinata replied

Jiraiya saw Naruto reach into his coat and he pulled out a Hitaite. Naruto bent his head and tied the Hitaite. When he looked up Jiraiya was able to see the symbol on it.

It was a Spiral.

"You've been busy' Jiraiya finally commented.

"You have no idea" Naruto chuckled. "The Whirlpool Country has risen from the Waves and the Village Hidden within the Vortex will wash over the world"

"Spare me the theatrics" Jiraiya said in a bored tone. He wanted to get a rise out of Naruto but he was disappointed when Naruto did nothing.

"A Sixth Hokage is needed Tsunade-same. You will not be strong enough to face the war that is coming. Please step aside. Do not die in battle like your predecessors." Hinata surprised Jiraiya with her frank speech.

"Who would I leave the Village to except to my own flesh and blood?" Tsunade asked her voice cracking slightly.

Over the years Jiraiya since their reunion Jiraiya had slowly realized that he knew Tsunade less and less. She still seemed like the woman he comforted on that night long ago when their son Minato was conceived. At this moment he allowed himself to see her clearly. She was tired. There was no doubt about that.

"Consider this my gift to you baachan." Naruto channelled chakra to his hand and it glowed red. When he approached Tsunade her Genjutsu was dispelled and she looked like her true self. Naruto reached out with his glowing hand and touched her forehead. The red chakra flowed over Tsunade and to his astonishment life returned to her features. The ravages of time and a hard life as a Shinobi were removed by Naruto's simple touch. "Take it and leave this place. Live the last years of your life in relative peace"

The gifts of the toads had already lengthened his life span and so he was not in need of Naruto's gift but he nonetheless knew that it was grudgingly extended to him as well.

"The storm that you mentioned, will you be the one to bring it to this world?"

"My plans are already in motion and my brethren support me. Akatsuki still remains a thorn in all of our sides and Kabuchimaru has started to move again. The time has come for me and him to complete that Jutsu"

"You mean to end the world..."

"Yes to end the world and bring true understanding. The losses have been heavy as you yourself can attest but I think we are finally at the end..."

"The end of all things." Hinata added.

"Well I have always wanted to travel the rest of the world" Jiraiya mused to himself. "How about it Tsunade? We take a boat, travel Over the Great Sea. One it will be one last great adventure for the Gallant Jiraiya and his Slug Princess."

"You insufferable old fool" she insulted. "Can't you see I am contemplating a major decision?"

"Everything that has a beginning has an end..." Hinata said cryptically.

"I've always liked endings" Naruto said to her.

"Why is that?"

"They always meant that we could start over" Naruto replied to his wife.

AN2: After that I still don't own Naruto. Sucks but that's life.


End file.
